Starting phenix.real_space_refine on Sun May 11 15:45:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v0g_42854/05_2025/8v0g_42854_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v0g_42854/05_2025/8v0g_42854.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v0g_42854/05_2025/8v0g_42854.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v0g_42854/05_2025/8v0g_42854.map" model { file = "/net/cci-nas-00/data/ceres_data/8v0g_42854/05_2025/8v0g_42854_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v0g_42854/05_2025/8v0g_42854_neut.cif" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 5328 2.51 5 N 1268 2.21 5 O 1465 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8106 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 8050 Classifications: {'peptide': 985} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 959} Chain breaks: 4 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'HIS%COO:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {'CLR': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.07, per 1000 atoms: 0.63 Number of scatterers: 8106 At special positions: 0 Unit cell: (89.88, 98.44, 126.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 45 16.00 O 1465 8.00 N 1268 7.00 C 5328 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1502 " - " ASN A 165 " " NAG A1503 " - " ASN A 294 " Time building additional restraints: 2.30 Conformation dependent library (CDL) restraints added in 955.9 milliseconds 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1880 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 8 sheets defined 71.7% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 3 through 35 removed outlier: 3.543A pdb=" N GLY A 30 " --> pdb=" O TYR A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 53 removed outlier: 3.610A pdb=" N PHE A 39 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 57 Processing helix chain 'A' and resid 62 through 68 Processing helix chain 'A' and resid 73 through 85 Processing helix chain 'A' and resid 103 through 120 removed outlier: 3.609A pdb=" N THR A 117 " --> pdb=" O PHE A 113 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 127 No H-bonds generated for 'chain 'A' and resid 125 through 127' Processing helix chain 'A' and resid 141 through 162 Processing helix chain 'A' and resid 294 through 299 Processing helix chain 'A' and resid 310 through 314 Processing helix chain 'A' and resid 320 through 325 removed outlier: 3.582A pdb=" N VAL A 324 " --> pdb=" O LYS A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 337 Processing helix chain 'A' and resid 338 through 345 Processing helix chain 'A' and resid 350 through 353 removed outlier: 3.714A pdb=" N CYS A 353 " --> pdb=" O GLU A 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 350 through 353' Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 369 through 373 Processing helix chain 'A' and resid 398 through 402 Processing helix chain 'A' and resid 435 through 453 Processing helix chain 'A' and resid 455 through 460 removed outlier: 3.569A pdb=" N ILE A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 491 Processing helix chain 'A' and resid 493 through 516 Processing helix chain 'A' and resid 524 through 550 removed outlier: 3.679A pdb=" N ALA A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 558 Processing helix chain 'A' and resid 559 through 582 removed outlier: 3.573A pdb=" N ASP A 570 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASP A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL A 572 " --> pdb=" O GLY A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 619 removed outlier: 4.751A pdb=" N LEU A 601 " --> pdb=" O LYS A 597 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ALA A 602 " --> pdb=" O ASP A 598 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 619 " --> pdb=" O LEU A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 645 Processing helix chain 'A' and resid 645 through 660 Processing helix chain 'A' and resid 663 through 673 Processing helix chain 'A' and resid 722 through 736 Processing helix chain 'A' and resid 1046 through 1050 Processing helix chain 'A' and resid 1057 through 1067 Processing helix chain 'A' and resid 1067 through 1074 Processing helix chain 'A' and resid 1074 through 1098 Processing helix chain 'A' and resid 1104 through 1109 Processing helix chain 'A' and resid 1113 through 1126 Processing helix chain 'A' and resid 1139 through 1150 removed outlier: 3.653A pdb=" N GLU A1150 " --> pdb=" O TYR A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1173 removed outlier: 3.641A pdb=" N SER A1173 " --> pdb=" O ILE A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1201 Processing helix chain 'A' and resid 1209 through 1218 Processing helix chain 'A' and resid 1218 through 1223 Processing helix chain 'A' and resid 1226 through 1241 Processing helix chain 'A' and resid 1241 through 1247 Processing helix chain 'A' and resid 1272 through 1287 Processing helix chain 'A' and resid 1290 through 1293 Processing helix chain 'A' and resid 1301 through 1335 removed outlier: 4.486A pdb=" N PHE A1305 " --> pdb=" O LEU A1301 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP A1309 " --> pdb=" O PHE A1305 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU A1310 " --> pdb=" O ASN A1306 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N SER A1311 " --> pdb=" O GLU A1307 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ILE A1313 " --> pdb=" O ASP A1309 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N GLU A1314 " --> pdb=" O GLU A1310 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A1317 " --> pdb=" O ILE A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1337 through 1362 Processing helix chain 'A' and resid 1367 through 1395 removed outlier: 3.876A pdb=" N VAL A1378 " --> pdb=" O LEU A1374 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLY A1379 " --> pdb=" O VAL A1375 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE A1380 " --> pdb=" O LEU A1376 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS A1384 " --> pdb=" O PHE A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1399 through 1428 removed outlier: 5.698A pdb=" N GLY A1413 " --> pdb=" O HIS A1409 " (cutoff:3.500A) Proline residue: A1414 - end of helix removed outlier: 4.111A pdb=" N THR A1428 " --> pdb=" O PHE A1424 " (cutoff:3.500A) Processing helix chain 'A' and resid 1429 through 1432 Processing helix chain 'A' and resid 1434 through 1457 Processing helix chain 'A' and resid 1457 through 1467 Processing sheet with id=AA1, first strand: chain 'A' and resid 403 through 404 removed outlier: 3.783A pdb=" N ALA A 422 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 123 Processing sheet with id=AA3, first strand: chain 'A' and resid 303 through 304 removed outlier: 6.460A pdb=" N LEU A1254 " --> pdb=" O LEU A1258 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N LEU A1258 " --> pdb=" O LEU A1254 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N HIS A1264 " --> pdb=" O VAL A1207 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL A1207 " --> pdb=" O HIS A1264 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N PHE A1266 " --> pdb=" O THR A1205 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 303 through 304 removed outlier: 6.460A pdb=" N LEU A1254 " --> pdb=" O LEU A1258 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N LEU A1258 " --> pdb=" O LEU A1254 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 355 through 356 Processing sheet with id=AA6, first strand: chain 'A' and resid 380 through 382 removed outlier: 3.789A pdb=" N ILE A 380 " --> pdb=" O ILE A 417 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 388 through 390 Processing sheet with id=AA8, first strand: chain 'A' and resid 1288 through 1289 533 hydrogen bonds defined for protein. 1518 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.93 Time building geometry restraints manager: 2.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2437 1.34 - 1.45: 1741 1.45 - 1.57: 4052 1.57 - 1.69: 0 1.69 - 1.81: 68 Bond restraints: 8298 Sorted by residual: bond pdb=" C PHE A1211 " pdb=" N THR A1212 " ideal model delta sigma weight residual 1.335 1.381 -0.047 1.25e-02 6.40e+03 1.40e+01 bond pdb=" C PHE A 733 " pdb=" N GLU A 734 " ideal model delta sigma weight residual 1.334 1.303 0.032 1.27e-02 6.20e+03 6.16e+00 bond pdb=" C PRO A 137 " pdb=" O PRO A 137 " ideal model delta sigma weight residual 1.246 1.229 0.017 8.50e-03 1.38e+04 3.93e+00 bond pdb=" CA ILE A 309 " pdb=" C ILE A 309 " ideal model delta sigma weight residual 1.524 1.504 0.021 1.05e-02 9.07e+03 3.83e+00 bond pdb=" CA PRO A 555 " pdb=" C PRO A 555 " ideal model delta sigma weight residual 1.517 1.534 -0.017 9.30e-03 1.16e+04 3.38e+00 ... (remaining 8293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 10139 1.53 - 3.06: 911 3.06 - 4.60: 131 4.60 - 6.13: 21 6.13 - 7.66: 6 Bond angle restraints: 11208 Sorted by residual: angle pdb=" CA VAL A1069 " pdb=" C VAL A1069 " pdb=" N PRO A1070 " ideal model delta sigma weight residual 120.83 117.37 3.46 6.10e-01 2.69e+00 3.22e+01 angle pdb=" CA VAL A 560 " pdb=" C VAL A 560 " pdb=" N PRO A 561 " ideal model delta sigma weight residual 120.83 117.57 3.26 6.10e-01 2.69e+00 2.86e+01 angle pdb=" N GLU A 176 " pdb=" CA GLU A 176 " pdb=" C GLU A 176 " ideal model delta sigma weight residual 111.71 105.77 5.94 1.15e+00 7.56e-01 2.67e+01 angle pdb=" N GLY A1102 " pdb=" CA GLY A1102 " pdb=" C GLY A1102 " ideal model delta sigma weight residual 112.18 118.49 -6.31 1.34e+00 5.57e-01 2.22e+01 angle pdb=" N LYS A1336 " pdb=" CA LYS A1336 " pdb=" C LYS A1336 " ideal model delta sigma weight residual 111.07 115.68 -4.61 1.07e+00 8.73e-01 1.86e+01 ... (remaining 11203 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.60: 4839 22.60 - 45.20: 129 45.20 - 67.80: 15 67.80 - 90.39: 6 90.39 - 112.99: 3 Dihedral angle restraints: 4992 sinusoidal: 2077 harmonic: 2915 Sorted by residual: dihedral pdb=" C1 NAG A1503 " pdb=" C5 NAG A1503 " pdb=" O5 NAG A1503 " pdb=" C6 NAG A1503 " ideal model delta sinusoidal sigma weight residual 171.16 -75.85 -112.99 1 3.00e+01 1.11e-03 1.48e+01 dihedral pdb=" C1 NAG A1503 " pdb=" C5 NAG A1503 " pdb=" O5 NAG A1503 " pdb=" C4 NAG A1503 " ideal model delta sinusoidal sigma weight residual -64.11 47.95 -112.06 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" C2 NAG A1503 " pdb=" C1 NAG A1503 " pdb=" O5 NAG A1503 " pdb=" C5 NAG A1503 " ideal model delta sinusoidal sigma weight residual -62.96 37.14 -100.10 1 3.00e+01 1.11e-03 1.25e+01 ... (remaining 4989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1123 0.069 - 0.139: 136 0.139 - 0.208: 3 0.208 - 0.277: 1 0.277 - 0.347: 2 Chirality restraints: 1265 Sorted by residual: chirality pdb=" C1 NAG A1503 " pdb=" ND2 ASN A 294 " pdb=" C2 NAG A1503 " pdb=" O5 NAG A1503 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" C13 CLR A1501 " pdb=" C12 CLR A1501 " pdb=" C14 CLR A1501 " pdb=" C17 CLR A1501 " both_signs ideal model delta sigma weight residual False -2.93 -2.62 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" C14 CLR A1501 " pdb=" C13 CLR A1501 " pdb=" C15 CLR A1501 " pdb=" C8 CLR A1501 " both_signs ideal model delta sigma weight residual False -2.32 -2.54 0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1262 not shown) Planarity restraints: 1384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1502 " 0.227 2.00e-02 2.50e+03 1.92e-01 4.62e+02 pdb=" C7 NAG A1502 " -0.049 2.00e-02 2.50e+03 pdb=" C8 NAG A1502 " -0.038 2.00e-02 2.50e+03 pdb=" N2 NAG A1502 " -0.314 2.00e-02 2.50e+03 pdb=" O7 NAG A1502 " 0.175 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1503 " -0.136 2.00e-02 2.50e+03 1.12e-01 1.57e+02 pdb=" C7 NAG A1503 " 0.038 2.00e-02 2.50e+03 pdb=" C8 NAG A1503 " -0.102 2.00e-02 2.50e+03 pdb=" N2 NAG A1503 " 0.179 2.00e-02 2.50e+03 pdb=" O7 NAG A1503 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A1459 " 0.024 5.00e-02 4.00e+02 3.67e-02 2.15e+00 pdb=" N PRO A1460 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A1460 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A1460 " 0.022 5.00e-02 4.00e+02 ... (remaining 1381 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.91: 4580 2.91 - 3.41: 9629 3.41 - 3.91: 14674 3.91 - 4.40: 18127 4.40 - 4.90: 26123 Nonbonded interactions: 73133 Sorted by model distance: nonbonded pdb=" OH TYR A 86 " pdb=" O ILE A 309 " model vdw 2.417 3.040 nonbonded pdb=" OD1 ASP A 123 " pdb=" OG SER A 125 " model vdw 2.429 3.040 nonbonded pdb=" O GLU A1150 " pdb=" C LYS A1151 " model vdw 2.429 3.270 nonbonded pdb=" O TYR A1059 " pdb=" OG SER A1062 " model vdw 2.436 3.040 nonbonded pdb=" OH TYR A1068 " pdb=" O SER A1456 " model vdw 2.438 3.040 ... (remaining 73128 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.880 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 8300 Z= 0.481 Angle : 0.950 7.659 11214 Z= 0.677 Chirality : 0.043 0.347 1265 Planarity : 0.007 0.192 1382 Dihedral : 10.812 112.992 3112 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 25.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.41 % Favored : 95.49 % Rotamer: Outliers : 0.88 % Allowed : 6.08 % Favored : 93.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.23), residues: 975 helix: -1.04 (0.18), residues: 629 sheet: -1.18 (0.68), residues: 51 loop : -1.30 (0.31), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1261 HIS 0.003 0.001 HIS A1195 PHE 0.010 0.001 PHE A 548 TYR 0.010 0.001 TYR A1136 ARG 0.003 0.000 ARG A 673 Details of bonding type rmsd link_NAG-ASN : bond 0.00283 ( 2) link_NAG-ASN : angle 1.70623 ( 6) hydrogen bonds : bond 0.17713 ( 529) hydrogen bonds : angle 7.91266 ( 1518) covalent geometry : bond 0.00629 ( 8298) covalent geometry : angle 0.94966 (11208) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 294 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 LEU cc_start: 0.9341 (tt) cc_final: 0.9114 (tt) REVERT: A 352 ILE cc_start: 0.9309 (OUTLIER) cc_final: 0.8966 (pp) REVERT: A 1222 LEU cc_start: 0.8751 (mp) cc_final: 0.8509 (mp) outliers start: 8 outliers final: 3 residues processed: 298 average time/residue: 0.1973 time to fit residues: 79.6758 Evaluate side-chains 159 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 155 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ASN Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 41 optimal weight: 0.4980 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 23 ASN ** A 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 ASN ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 HIS A 431 ASN ** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 577 ASN ** A 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1055 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1177 ASN A1184 ASN A1201 GLN A1228 GLN A1255 ASN A1291 ASN A1293 ASN ** A1306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.093090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.076744 restraints weight = 17243.770| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.15 r_work: 0.2925 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8300 Z= 0.179 Angle : 0.671 9.816 11214 Z= 0.352 Chirality : 0.043 0.165 1265 Planarity : 0.005 0.045 1382 Dihedral : 7.453 97.674 1176 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.76 % Allowed : 13.37 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.26), residues: 975 helix: 1.57 (0.20), residues: 621 sheet: -0.53 (0.70), residues: 52 loop : -0.13 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 726 HIS 0.007 0.002 HIS A1417 PHE 0.023 0.002 PHE A 733 TYR 0.016 0.002 TYR A 304 ARG 0.004 0.000 ARG A 89 Details of bonding type rmsd link_NAG-ASN : bond 0.00378 ( 2) link_NAG-ASN : angle 1.29874 ( 6) hydrogen bonds : bond 0.05931 ( 529) hydrogen bonds : angle 5.13735 ( 1518) covalent geometry : bond 0.00390 ( 8298) covalent geometry : angle 0.67021 (11208) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 192 time to evaluate : 0.861 Fit side-chains revert: symmetry clash REVERT: A 124 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9007 (mp) REVERT: A 152 ILE cc_start: 0.9364 (tp) cc_final: 0.9119 (pt) REVERT: A 336 GLU cc_start: 0.9106 (tp30) cc_final: 0.8602 (tt0) REVERT: A 360 CYS cc_start: 0.8961 (m) cc_final: 0.8468 (m) REVERT: A 543 SER cc_start: 0.9081 (m) cc_final: 0.8779 (p) REVERT: A 1055 ASN cc_start: 0.8296 (m-40) cc_final: 0.8036 (m-40) REVERT: A 1278 LYS cc_start: 0.9186 (tppp) cc_final: 0.8947 (tppp) REVERT: A 1352 ASP cc_start: 0.8801 (m-30) cc_final: 0.8586 (m-30) REVERT: A 1398 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8157 (mtm180) outliers start: 25 outliers final: 9 residues processed: 206 average time/residue: 0.1491 time to fit residues: 44.8886 Evaluate side-chains 158 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1267 GLN Chi-restraints excluded: chain A residue 1303 SER Chi-restraints excluded: chain A residue 1334 ILE Chi-restraints excluded: chain A residue 1398 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 56 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 23 optimal weight: 0.3980 chunk 26 optimal weight: 7.9990 chunk 65 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 HIS A 133 ASN ** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1055 ASN ** A1269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1394 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.090041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.074035 restraints weight = 17956.742| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 3.26 r_work: 0.2900 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8300 Z= 0.153 Angle : 0.586 9.494 11214 Z= 0.310 Chirality : 0.042 0.207 1265 Planarity : 0.004 0.042 1382 Dihedral : 6.916 89.211 1170 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 3.20 % Allowed : 14.70 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.27), residues: 975 helix: 2.12 (0.20), residues: 617 sheet: -0.47 (0.66), residues: 52 loop : 0.25 (0.36), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1261 HIS 0.005 0.001 HIS A1195 PHE 0.017 0.002 PHE A 733 TYR 0.015 0.001 TYR A 304 ARG 0.003 0.000 ARG A 89 Details of bonding type rmsd link_NAG-ASN : bond 0.00132 ( 2) link_NAG-ASN : angle 1.48139 ( 6) hydrogen bonds : bond 0.05073 ( 529) hydrogen bonds : angle 4.66854 ( 1518) covalent geometry : bond 0.00347 ( 8298) covalent geometry : angle 0.58553 (11208) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 167 time to evaluate : 0.949 Fit side-chains REVERT: A 19 ASP cc_start: 0.9282 (m-30) cc_final: 0.8810 (m-30) REVERT: A 52 CYS cc_start: 0.8982 (m) cc_final: 0.8492 (t) REVERT: A 145 LYS cc_start: 0.9191 (mmmt) cc_final: 0.8705 (mppt) REVERT: A 146 GLU cc_start: 0.9220 (mm-30) cc_final: 0.8805 (mm-30) REVERT: A 336 GLU cc_start: 0.9075 (tp30) cc_final: 0.8619 (tt0) REVERT: A 360 CYS cc_start: 0.8822 (m) cc_final: 0.8605 (m) REVERT: A 543 SER cc_start: 0.9097 (m) cc_final: 0.8798 (p) REVERT: A 598 ASP cc_start: 0.8953 (m-30) cc_final: 0.8720 (m-30) REVERT: A 1278 LYS cc_start: 0.9177 (tppp) cc_final: 0.8833 (tppp) REVERT: A 1352 ASP cc_start: 0.8946 (m-30) cc_final: 0.8674 (m-30) REVERT: A 1398 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8218 (mtm180) REVERT: A 1444 LEU cc_start: 0.9052 (tp) cc_final: 0.8796 (tp) outliers start: 29 outliers final: 13 residues processed: 184 average time/residue: 0.1652 time to fit residues: 43.8005 Evaluate side-chains 159 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1101 LYS Chi-restraints excluded: chain A residue 1243 VAL Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1267 GLN Chi-restraints excluded: chain A residue 1398 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 44 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 16 optimal weight: 0.1980 chunk 93 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 97 optimal weight: 0.0970 chunk 64 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 62 optimal weight: 0.0980 chunk 2 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 514 ASN ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1055 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.092142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.075890 restraints weight = 17435.246| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 3.22 r_work: 0.2913 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8300 Z= 0.124 Angle : 0.564 10.471 11214 Z= 0.294 Chirality : 0.040 0.173 1265 Planarity : 0.004 0.039 1382 Dihedral : 6.444 79.249 1170 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 3.54 % Allowed : 16.35 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.26), residues: 975 helix: 2.20 (0.20), residues: 619 sheet: -0.34 (0.64), residues: 52 loop : 0.22 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1261 HIS 0.004 0.001 HIS A1195 PHE 0.024 0.001 PHE A 508 TYR 0.012 0.001 TYR A 304 ARG 0.004 0.000 ARG A1147 Details of bonding type rmsd link_NAG-ASN : bond 0.00053 ( 2) link_NAG-ASN : angle 1.99995 ( 6) hydrogen bonds : bond 0.04633 ( 529) hydrogen bonds : angle 4.50338 ( 1518) covalent geometry : bond 0.00266 ( 8298) covalent geometry : angle 0.56229 (11208) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 173 time to evaluate : 0.868 Fit side-chains revert: symmetry clash REVERT: A 19 ASP cc_start: 0.9305 (m-30) cc_final: 0.8791 (m-30) REVERT: A 52 CYS cc_start: 0.8877 (m) cc_final: 0.8421 (t) REVERT: A 142 HIS cc_start: 0.8388 (t-170) cc_final: 0.7983 (t-170) REVERT: A 145 LYS cc_start: 0.9212 (mmmt) cc_final: 0.8664 (mppt) REVERT: A 146 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8689 (mm-30) REVERT: A 336 GLU cc_start: 0.9066 (tp30) cc_final: 0.8698 (pt0) REVERT: A 493 ASP cc_start: 0.8093 (t0) cc_final: 0.7644 (t70) REVERT: A 543 SER cc_start: 0.9071 (m) cc_final: 0.8765 (p) REVERT: A 594 MET cc_start: 0.8842 (mtp) cc_final: 0.8422 (mtp) REVERT: A 598 ASP cc_start: 0.8920 (m-30) cc_final: 0.8668 (m-30) REVERT: A 721 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8297 (tp) REVERT: A 1099 MET cc_start: 0.8571 (tmm) cc_final: 0.8286 (ttp) REVERT: A 1171 MET cc_start: 0.8888 (pmm) cc_final: 0.8652 (pmm) REVERT: A 1278 LYS cc_start: 0.9167 (tppp) cc_final: 0.8791 (tppp) REVERT: A 1398 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8247 (mtm180) REVERT: A 1443 THR cc_start: 0.9697 (m) cc_final: 0.9435 (p) REVERT: A 1444 LEU cc_start: 0.9114 (tp) cc_final: 0.8853 (tp) outliers start: 32 outliers final: 15 residues processed: 193 average time/residue: 0.1553 time to fit residues: 43.4545 Evaluate side-chains 159 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 1101 LYS Chi-restraints excluded: chain A residue 1243 VAL Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1398 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1055 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.091142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.075052 restraints weight = 17613.943| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 3.20 r_work: 0.2903 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8300 Z= 0.148 Angle : 0.573 11.017 11214 Z= 0.298 Chirality : 0.041 0.175 1265 Planarity : 0.004 0.038 1382 Dihedral : 5.925 66.137 1170 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.31 % Allowed : 17.02 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.27), residues: 975 helix: 2.21 (0.20), residues: 618 sheet: -0.32 (0.64), residues: 52 loop : 0.31 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1261 HIS 0.004 0.001 HIS A1195 PHE 0.023 0.001 PHE A 733 TYR 0.013 0.001 TYR A 369 ARG 0.003 0.000 ARG A1147 Details of bonding type rmsd link_NAG-ASN : bond 0.00136 ( 2) link_NAG-ASN : angle 2.52734 ( 6) hydrogen bonds : bond 0.04591 ( 529) hydrogen bonds : angle 4.43324 ( 1518) covalent geometry : bond 0.00337 ( 8298) covalent geometry : angle 0.57034 (11208) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: A 19 ASP cc_start: 0.9299 (m-30) cc_final: 0.8909 (m-30) REVERT: A 52 CYS cc_start: 0.8797 (m) cc_final: 0.8410 (t) REVERT: A 67 TYR cc_start: 0.9161 (m-80) cc_final: 0.8836 (m-80) REVERT: A 142 HIS cc_start: 0.8357 (t-170) cc_final: 0.7992 (t-170) REVERT: A 145 LYS cc_start: 0.9253 (mmmt) cc_final: 0.8922 (tppt) REVERT: A 146 GLU cc_start: 0.9192 (mm-30) cc_final: 0.8717 (mm-30) REVERT: A 156 GLU cc_start: 0.9128 (tp30) cc_final: 0.8835 (tp30) REVERT: A 160 LYS cc_start: 0.9575 (ttmm) cc_final: 0.9370 (ttmm) REVERT: A 336 GLU cc_start: 0.9083 (tp30) cc_final: 0.8663 (pt0) REVERT: A 360 CYS cc_start: 0.8234 (m) cc_final: 0.7690 (p) REVERT: A 493 ASP cc_start: 0.8164 (t0) cc_final: 0.7854 (t0) REVERT: A 543 SER cc_start: 0.9054 (m) cc_final: 0.8760 (p) REVERT: A 598 ASP cc_start: 0.8899 (m-30) cc_final: 0.8636 (m-30) REVERT: A 721 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8292 (tp) REVERT: A 1099 MET cc_start: 0.8694 (tmm) cc_final: 0.8251 (ttp) REVERT: A 1278 LYS cc_start: 0.9184 (tppp) cc_final: 0.8803 (tppp) REVERT: A 1398 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8232 (mtm180) REVERT: A 1444 LEU cc_start: 0.9028 (tp) cc_final: 0.8797 (tp) outliers start: 30 outliers final: 18 residues processed: 179 average time/residue: 0.1658 time to fit residues: 42.6425 Evaluate side-chains 164 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1101 LYS Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1243 VAL Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1267 GLN Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1398 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 21 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 81 optimal weight: 0.4980 chunk 88 optimal weight: 0.8980 chunk 62 optimal weight: 0.0870 chunk 60 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1055 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 GLN ** A1209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.091602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.076050 restraints weight = 17552.808| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 3.19 r_work: 0.2916 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8300 Z= 0.135 Angle : 0.573 10.799 11214 Z= 0.297 Chirality : 0.040 0.182 1265 Planarity : 0.003 0.036 1382 Dihedral : 5.130 60.971 1170 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.43 % Allowed : 17.46 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.27), residues: 975 helix: 2.19 (0.21), residues: 620 sheet: -0.32 (0.64), residues: 52 loop : 0.27 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1261 HIS 0.003 0.001 HIS A1195 PHE 0.020 0.001 PHE A 733 TYR 0.017 0.001 TYR A 55 ARG 0.004 0.000 ARG A1223 Details of bonding type rmsd link_NAG-ASN : bond 0.00276 ( 2) link_NAG-ASN : angle 3.66256 ( 6) hydrogen bonds : bond 0.04457 ( 529) hydrogen bonds : angle 4.36395 ( 1518) covalent geometry : bond 0.00302 ( 8298) covalent geometry : angle 0.56659 (11208) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: A 19 ASP cc_start: 0.9289 (m-30) cc_final: 0.8770 (m-30) REVERT: A 52 CYS cc_start: 0.8775 (m) cc_final: 0.8521 (t) REVERT: A 67 TYR cc_start: 0.9191 (m-80) cc_final: 0.8830 (m-80) REVERT: A 68 SER cc_start: 0.8845 (OUTLIER) cc_final: 0.8597 (p) REVERT: A 142 HIS cc_start: 0.8273 (t-170) cc_final: 0.7863 (t-170) REVERT: A 145 LYS cc_start: 0.9274 (mmmt) cc_final: 0.8908 (tppt) REVERT: A 146 GLU cc_start: 0.9168 (mm-30) cc_final: 0.8647 (mm-30) REVERT: A 156 GLU cc_start: 0.9086 (tp30) cc_final: 0.8786 (tp30) REVERT: A 160 LYS cc_start: 0.9581 (ttmm) cc_final: 0.9353 (ttmm) REVERT: A 336 GLU cc_start: 0.9089 (tp30) cc_final: 0.8677 (pt0) REVERT: A 360 CYS cc_start: 0.8229 (m) cc_final: 0.7759 (p) REVERT: A 493 ASP cc_start: 0.8226 (t0) cc_final: 0.7930 (t0) REVERT: A 543 SER cc_start: 0.9107 (m) cc_final: 0.8767 (p) REVERT: A 594 MET cc_start: 0.8829 (mtp) cc_final: 0.8417 (mtp) REVERT: A 598 ASP cc_start: 0.8877 (m-30) cc_final: 0.8614 (m-30) REVERT: A 721 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8310 (tp) REVERT: A 1171 MET cc_start: 0.8911 (pmm) cc_final: 0.8708 (pmm) REVERT: A 1278 LYS cc_start: 0.9136 (tppp) cc_final: 0.8739 (tppp) REVERT: A 1398 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8218 (mtm180) REVERT: A 1443 THR cc_start: 0.9701 (m) cc_final: 0.9441 (p) REVERT: A 1444 LEU cc_start: 0.9047 (tp) cc_final: 0.8824 (tp) outliers start: 31 outliers final: 17 residues processed: 184 average time/residue: 0.1818 time to fit residues: 48.9085 Evaluate side-chains 168 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1101 LYS Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1243 VAL Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1267 GLN Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1398 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 73 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1055 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.089184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.072534 restraints weight = 18163.335| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 3.29 r_work: 0.2933 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.4975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8300 Z= 0.149 Angle : 0.585 10.114 11214 Z= 0.303 Chirality : 0.041 0.192 1265 Planarity : 0.004 0.036 1382 Dihedral : 4.532 57.496 1170 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.20 % Allowed : 19.01 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.27), residues: 975 helix: 2.17 (0.21), residues: 620 sheet: -0.23 (0.67), residues: 52 loop : 0.35 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1261 HIS 0.004 0.001 HIS A1195 PHE 0.028 0.001 PHE A 513 TYR 0.011 0.001 TYR A 304 ARG 0.004 0.000 ARG A1147 Details of bonding type rmsd link_NAG-ASN : bond 0.00484 ( 2) link_NAG-ASN : angle 4.24858 ( 6) hydrogen bonds : bond 0.04557 ( 529) hydrogen bonds : angle 4.35850 ( 1518) covalent geometry : bond 0.00340 ( 8298) covalent geometry : angle 0.57730 (11208) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 0.956 Fit side-chains revert: symmetry clash REVERT: A 19 ASP cc_start: 0.9245 (m-30) cc_final: 0.8726 (m-30) REVERT: A 52 CYS cc_start: 0.8840 (m) cc_final: 0.8566 (t) REVERT: A 67 TYR cc_start: 0.9270 (m-80) cc_final: 0.8950 (m-80) REVERT: A 68 SER cc_start: 0.8922 (OUTLIER) cc_final: 0.8702 (p) REVERT: A 142 HIS cc_start: 0.8193 (t-170) cc_final: 0.7831 (t-170) REVERT: A 145 LYS cc_start: 0.9335 (mmmt) cc_final: 0.8943 (tppt) REVERT: A 146 GLU cc_start: 0.9094 (mm-30) cc_final: 0.8593 (mm-30) REVERT: A 156 GLU cc_start: 0.9037 (tp30) cc_final: 0.8762 (tp30) REVERT: A 160 LYS cc_start: 0.9587 (ttmm) cc_final: 0.9370 (ttmm) REVERT: A 336 GLU cc_start: 0.9048 (tp30) cc_final: 0.8645 (pt0) REVERT: A 360 CYS cc_start: 0.8174 (m) cc_final: 0.7713 (p) REVERT: A 367 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8849 (tt) REVERT: A 493 ASP cc_start: 0.8302 (t0) cc_final: 0.8038 (t0) REVERT: A 509 MET cc_start: 0.8712 (mmm) cc_final: 0.8440 (tmm) REVERT: A 543 SER cc_start: 0.9171 (m) cc_final: 0.8848 (p) REVERT: A 721 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8354 (tp) REVERT: A 1147 ARG cc_start: 0.8644 (mmt90) cc_final: 0.8340 (mmt90) REVERT: A 1278 LYS cc_start: 0.9120 (tppp) cc_final: 0.8720 (tppp) REVERT: A 1352 ASP cc_start: 0.9077 (m-30) cc_final: 0.8803 (m-30) REVERT: A 1398 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8243 (mtm180) REVERT: A 1444 LEU cc_start: 0.9222 (tp) cc_final: 0.9016 (tp) outliers start: 29 outliers final: 15 residues processed: 182 average time/residue: 0.1626 time to fit residues: 42.8483 Evaluate side-chains 173 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1243 VAL Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1267 GLN Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1398 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 59 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1055 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.089087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.072437 restraints weight = 18203.085| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 3.29 r_work: 0.2922 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.5093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8300 Z= 0.150 Angle : 0.583 9.643 11214 Z= 0.301 Chirality : 0.041 0.176 1265 Planarity : 0.003 0.035 1382 Dihedral : 4.358 53.462 1170 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.65 % Allowed : 20.33 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.27), residues: 975 helix: 2.19 (0.21), residues: 620 sheet: -0.23 (0.67), residues: 52 loop : 0.40 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1261 HIS 0.004 0.001 HIS A1195 PHE 0.036 0.001 PHE A 513 TYR 0.011 0.001 TYR A 304 ARG 0.005 0.000 ARG A1147 Details of bonding type rmsd link_NAG-ASN : bond 0.00277 ( 2) link_NAG-ASN : angle 3.45429 ( 6) hydrogen bonds : bond 0.04495 ( 529) hydrogen bonds : angle 4.34701 ( 1518) covalent geometry : bond 0.00344 ( 8298) covalent geometry : angle 0.57789 (11208) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: A 19 ASP cc_start: 0.9239 (m-30) cc_final: 0.8734 (m-30) REVERT: A 52 CYS cc_start: 0.8863 (m) cc_final: 0.8569 (t) REVERT: A 67 TYR cc_start: 0.9277 (m-80) cc_final: 0.8986 (m-80) REVERT: A 68 SER cc_start: 0.8901 (OUTLIER) cc_final: 0.8688 (p) REVERT: A 142 HIS cc_start: 0.8177 (t-170) cc_final: 0.7832 (t-170) REVERT: A 145 LYS cc_start: 0.9340 (mmmt) cc_final: 0.8967 (tppt) REVERT: A 146 GLU cc_start: 0.9115 (mm-30) cc_final: 0.8630 (mm-30) REVERT: A 336 GLU cc_start: 0.9105 (tp30) cc_final: 0.8718 (pt0) REVERT: A 360 CYS cc_start: 0.8255 (m) cc_final: 0.7788 (p) REVERT: A 457 ASP cc_start: 0.9111 (p0) cc_final: 0.8778 (m-30) REVERT: A 460 GLN cc_start: 0.7986 (mt0) cc_final: 0.7623 (mp10) REVERT: A 493 ASP cc_start: 0.8290 (t0) cc_final: 0.8055 (t0) REVERT: A 509 MET cc_start: 0.8660 (mmm) cc_final: 0.8420 (tmm) REVERT: A 543 SER cc_start: 0.9137 (m) cc_final: 0.8797 (p) REVERT: A 721 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8329 (tp) REVERT: A 1278 LYS cc_start: 0.9133 (tppp) cc_final: 0.8739 (tppp) REVERT: A 1398 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8269 (mtm180) outliers start: 24 outliers final: 16 residues processed: 182 average time/residue: 0.1660 time to fit residues: 43.4934 Evaluate side-chains 177 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1243 VAL Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1267 GLN Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1398 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 76 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 53 optimal weight: 0.1980 chunk 36 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 54 optimal weight: 0.0870 chunk 67 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1055 ASN ** A1209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.091372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.075246 restraints weight = 18219.872| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.27 r_work: 0.2947 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8300 Z= 0.130 Angle : 0.592 9.729 11214 Z= 0.306 Chirality : 0.040 0.199 1265 Planarity : 0.003 0.036 1382 Dihedral : 4.269 49.544 1170 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.43 % Allowed : 21.33 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.27), residues: 975 helix: 2.22 (0.21), residues: 620 sheet: -0.10 (0.68), residues: 52 loop : 0.45 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1261 HIS 0.004 0.001 HIS A1195 PHE 0.029 0.001 PHE A 513 TYR 0.010 0.001 TYR A 26 ARG 0.005 0.000 ARG A1147 Details of bonding type rmsd link_NAG-ASN : bond 0.00066 ( 2) link_NAG-ASN : angle 2.93740 ( 6) hydrogen bonds : bond 0.04349 ( 529) hydrogen bonds : angle 4.29122 ( 1518) covalent geometry : bond 0.00292 ( 8298) covalent geometry : angle 0.58775 (11208) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: A 19 ASP cc_start: 0.9218 (m-30) cc_final: 0.8715 (m-30) REVERT: A 52 CYS cc_start: 0.8800 (m) cc_final: 0.8548 (t) REVERT: A 67 TYR cc_start: 0.9273 (m-80) cc_final: 0.8975 (m-80) REVERT: A 68 SER cc_start: 0.8889 (OUTLIER) cc_final: 0.8678 (p) REVERT: A 142 HIS cc_start: 0.8085 (t-170) cc_final: 0.7827 (t-170) REVERT: A 145 LYS cc_start: 0.9346 (mmmt) cc_final: 0.8890 (tppt) REVERT: A 146 GLU cc_start: 0.9086 (mm-30) cc_final: 0.8608 (mm-30) REVERT: A 336 GLU cc_start: 0.9098 (tp30) cc_final: 0.8742 (pt0) REVERT: A 360 CYS cc_start: 0.8176 (m) cc_final: 0.7703 (p) REVERT: A 457 ASP cc_start: 0.9060 (p0) cc_final: 0.8830 (m-30) REVERT: A 460 GLN cc_start: 0.7887 (mt0) cc_final: 0.7496 (mp10) REVERT: A 493 ASP cc_start: 0.8258 (t0) cc_final: 0.7923 (t0) REVERT: A 509 MET cc_start: 0.8689 (mmm) cc_final: 0.8427 (tmm) REVERT: A 543 SER cc_start: 0.9128 (m) cc_final: 0.8795 (p) REVERT: A 658 GLU cc_start: 0.9024 (tt0) cc_final: 0.8701 (tp30) REVERT: A 721 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8337 (tp) REVERT: A 1278 LYS cc_start: 0.9114 (tppp) cc_final: 0.8687 (tppp) REVERT: A 1352 ASP cc_start: 0.9075 (m-30) cc_final: 0.8796 (m-30) REVERT: A 1371 MET cc_start: 0.9016 (mmp) cc_final: 0.8751 (mmm) outliers start: 22 outliers final: 14 residues processed: 187 average time/residue: 0.1545 time to fit residues: 42.2223 Evaluate side-chains 178 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1243 VAL Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1267 GLN Chi-restraints excluded: chain A residue 1344 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 89 optimal weight: 0.9980 chunk 64 optimal weight: 0.0370 chunk 68 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 97 optimal weight: 0.2980 chunk 13 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 58 optimal weight: 0.0670 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.090992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.074571 restraints weight = 18151.283| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.29 r_work: 0.2957 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.5389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8300 Z= 0.122 Angle : 0.580 9.684 11214 Z= 0.300 Chirality : 0.040 0.198 1265 Planarity : 0.003 0.036 1382 Dihedral : 4.185 45.131 1170 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.88 % Allowed : 21.88 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.27), residues: 975 helix: 2.22 (0.21), residues: 621 sheet: 0.00 (0.67), residues: 52 loop : 0.49 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1261 HIS 0.003 0.001 HIS A 142 PHE 0.026 0.001 PHE A 733 TYR 0.010 0.001 TYR A 26 ARG 0.005 0.000 ARG A1147 Details of bonding type rmsd link_NAG-ASN : bond 0.00071 ( 2) link_NAG-ASN : angle 2.59899 ( 6) hydrogen bonds : bond 0.04218 ( 529) hydrogen bonds : angle 4.24969 ( 1518) covalent geometry : bond 0.00269 ( 8298) covalent geometry : angle 0.57682 (11208) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 179 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: A 19 ASP cc_start: 0.9234 (m-30) cc_final: 0.8731 (m-30) REVERT: A 52 CYS cc_start: 0.8771 (m) cc_final: 0.8539 (t) REVERT: A 67 TYR cc_start: 0.9266 (m-80) cc_final: 0.8937 (m-80) REVERT: A 68 SER cc_start: 0.8847 (OUTLIER) cc_final: 0.8544 (p) REVERT: A 83 ASP cc_start: 0.9195 (m-30) cc_final: 0.8856 (m-30) REVERT: A 142 HIS cc_start: 0.8099 (t-170) cc_final: 0.7889 (t-170) REVERT: A 145 LYS cc_start: 0.9335 (mmmt) cc_final: 0.8956 (tppt) REVERT: A 146 GLU cc_start: 0.9083 (mm-30) cc_final: 0.8580 (mm-30) REVERT: A 336 GLU cc_start: 0.9065 (tp30) cc_final: 0.8820 (pt0) REVERT: A 360 CYS cc_start: 0.8181 (m) cc_final: 0.7689 (p) REVERT: A 457 ASP cc_start: 0.9027 (p0) cc_final: 0.8663 (m-30) REVERT: A 460 GLN cc_start: 0.7916 (mt0) cc_final: 0.7491 (mp10) REVERT: A 493 ASP cc_start: 0.8289 (t0) cc_final: 0.7958 (t0) REVERT: A 508 PHE cc_start: 0.9117 (t80) cc_final: 0.8741 (t80) REVERT: A 509 MET cc_start: 0.8704 (mmm) cc_final: 0.8429 (tmm) REVERT: A 543 SER cc_start: 0.9120 (m) cc_final: 0.8783 (p) REVERT: A 658 GLU cc_start: 0.9015 (tt0) cc_final: 0.8691 (tp30) REVERT: A 721 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8324 (tp) REVERT: A 1147 ARG cc_start: 0.8648 (mmt90) cc_final: 0.8416 (mmt90) REVERT: A 1278 LYS cc_start: 0.9068 (tppp) cc_final: 0.8632 (tppp) REVERT: A 1371 MET cc_start: 0.8949 (mmp) cc_final: 0.8701 (mmm) REVERT: A 1398 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8252 (mtm180) outliers start: 17 outliers final: 13 residues processed: 191 average time/residue: 0.1690 time to fit residues: 46.4524 Evaluate side-chains 182 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1243 VAL Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1267 GLN Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1398 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.3980 chunk 49 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.090544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.074010 restraints weight = 18289.180| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 3.24 r_work: 0.2954 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.5462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8300 Z= 0.135 Angle : 0.606 9.862 11214 Z= 0.309 Chirality : 0.041 0.190 1265 Planarity : 0.004 0.036 1382 Dihedral : 4.151 43.104 1170 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.99 % Allowed : 22.76 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.27), residues: 975 helix: 2.22 (0.21), residues: 621 sheet: 0.05 (0.68), residues: 52 loop : 0.53 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1261 HIS 0.004 0.001 HIS A1195 PHE 0.026 0.001 PHE A 733 TYR 0.013 0.001 TYR A1094 ARG 0.004 0.000 ARG A1147 Details of bonding type rmsd link_NAG-ASN : bond 0.00071 ( 2) link_NAG-ASN : angle 2.45310 ( 6) hydrogen bonds : bond 0.04252 ( 529) hydrogen bonds : angle 4.25531 ( 1518) covalent geometry : bond 0.00309 ( 8298) covalent geometry : angle 0.60383 (11208) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3680.06 seconds wall clock time: 64 minutes 57.51 seconds (3897.51 seconds total)